data_50341 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Assignment of base 15N and 1H chemical shifts for <3_s2m> ; _BMRB_accession_number 50341 _BMRB_flat_file_name bmr50341.str _Entry_type original _Submission_date 2020-06-23 _Accession_date 2020-06-23 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details . loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Schwalbe Harald . . 2 Richter Christian . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 29 "15N chemical shifts" 34 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2020-12-18 update BMRB 'update entry citation' 2020-07-10 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 50339 'chemical shifts of the 5_SL5B+C' 50340 'chemical shifts of the 5_SL5stem' 50342 'chemical shifts of the 3_SL1' 50343 'chemical shifts of the 2_SL3' 50344 'chemical shifts of the 5_SL2+3' 50346 'chemical shifts of the 5_SL5a' 50347 'chemical shifts of the 5_SL4' 50348 'chemical shifts of the PK (Pseudoknot)' 50349 'chemical shifts of the 5_SL1' 50350 'chemical shifts of the 3_SL3base' 50351 'chemical shifts of the 5_SL6' 50352 'chemical shifts of the 5_SL8' stop_ _Original_release_date 2020-06-23 save_ ############################# # Citation for this entry # ############################# save_citations_1 _Saveframe_category entry_citation _Citation_full . _Citation_title ; Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 33167030 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Wacker Anna . . 2 Weigand Julia E. . 3 Akabayov Sabine R. . 4 Altincekic Nadide . . 5 'Kaur Bains' Jasleen . . 6 Banijamali Elnaz . . 7 Binas Oliver . . 8 Castillo-Martinez Jesus . . 9 Cetiner Erhan . . 10 Ceylan Betul . . 11 Chiu Liang-Yuan . . 12 Davila-Calderon Jesse . . 13 'De Jesus' Vanessa . . 14 Dhamotharan Karthikeyan . . 15 Duchardt-Ferner Elke . . 16 Ferner Jan . . 17 Frydman Lucio . . 18 Furtig Boris . . 19 Gallego Jose . . 20 Grun 'J. Tassilo' . . 21 Hacker Carolin . . 22 Haddad Christina . . 23 Hahnke Martin . . 24 Hengesbach Martin . . 25 Hiller Fabian . . 26 Hohmann Katharina F. . 27 Hymon Daniel . . 28 Jonker Henry . . 29 Keller Heiko . . 30 Knezic Bozana . . 31 Landgraf Tom . . 32 Lohr Frank . . 33 Luo Luke . . 34 Mertinkus Klara R. . 35 Muhs Christina . . 36 Novakovic Mihajlo . . 37 Oxenfarth Andreas . . 38 Palomino-Schatzlein Martina . . 39 Petzold Katja . . 40 Peter Stephen A. . 41 Pyper Dennis J. . 42 Qureshi Nusrat S. . 43 Riad Magdalena . . 44 Richter Christian . . 45 Saxena Krishna . . 46 Schamber Tatjana . . 47 Scherf Tali . . 48 Schlagnitweit Judith . . 49 Schlundt Andreas . . 50 Schnieders Robbin . . 51 Schwalbe Harald . . 52 Simba-Lahuasi Alvaro . . 53 Sreeramulu Sridhar . . 54 Stirnal Elke . . 55 Sudakov Alexey . . 56 Tants Jan-Niklas . . 57 Tolbert Blanton S. . 58 Vogele Jenny . . 59 Weiss Lena . . 60 Wirmer-Bartoschek Julia . . 61 'Wirtz Martin' Maria A. . 62 Wohnert Jens . . 63 Zetzsche Heidi . . stop_ _Journal_abbreviation 'Nucleic Acids Res.' _Journal_name_full 'Nucleic acids research' _Journal_volume 48 _Journal_issue 22 _Journal_ISSN 1362-4962 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 12415 _Page_last 12435 _Year 2020 _Details . save_ ################################## # Molecular system description # ################################## save_assembly_1 _Saveframe_category molecular_system _Mol_system_name 3_s2m _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 3_s2m $entity_1 stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_entity_1 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common entity_1 _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 45 _Mol_residue_sequence ; GGUUCACCGAGGCCACGCGG AGUACGAUCGAGUGUACAGU GAACC ; loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 -1 G 2 -2 G 3 29728 U 4 29729 U 5 29730 C 6 29731 A 7 29732 C 8 29733 C 9 29734 G 10 29735 A 11 29736 G 12 29737 G 13 29738 C 14 29739 C 15 29740 A 16 29741 C 17 29742 G 18 29743 C 19 29744 G 20 29745 G 21 29746 A 22 29747 G 23 29748 U 24 29749 A 25 29750 C 26 29751 G 27 29752 A 28 29753 U 29 29754 C 30 29755 G 31 29756 A 32 29757 G 33 29758 U 34 29759 G 35 29760 U 36 29761 A 37 29762 C 38 29763 A 39 29764 G 40 29765 U 41 29766 G 42 29767 A 43 29768 A 44 1 C 45 2 C stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ #################### # Natural source # #################### save_natural_source_1 _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species _Strain $entity_1 SARS-CoV-2 2697049 Viruses . Betacoronavirus HCoV-SARS SARS-CoV-2 stop_ save_ ######################### # Experimental source # ######################### save_experimental_source_1 _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_name $entity_1 'reverse transcriptase' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $entity_1 0.39 mM [U-15N] 'potassium phosphate' 25 mM 'natural abundance' KCl 50 mM 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Saveframe_category software _Name LOGS _Version 2.2 loop_ _Task collection stop_ _Details . save_ save_software_2 _Saveframe_category software _Name SPARKY _Version 3.114 loop_ _Task 'chemical shift assignment' 'peak picking' stop_ _Details . save_ save_software_3 _Saveframe_category software _Name TOPSPIN _Version 3.6.2 loop_ _Task collection stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model 'Bruker Avance III HD 600 MHz' _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_HNN-COSY[15N]_1 _Saveframe_category NMR_applied_experiment _Experiment_name HNN-COSY[15N] _Sample_label $sample_1 save_ save_NOESY[15N]CPMG_2 _Saveframe_category NMR_applied_experiment _Experiment_name NOESY[15N]CPMG _Sample_label $sample_1 save_ save_HSQC[15N]-Amino_3 _Saveframe_category NMR_applied_experiment _Experiment_name HSQC[15N]-Amino _Sample_label $sample_1 save_ save_HSQC[15N]-2J_4 _Saveframe_category NMR_applied_experiment _Experiment_name HSQC[15N]-2J _Sample_label $sample_1 save_ save_TROSY[15N]_5 _Saveframe_category NMR_applied_experiment _Experiment_name TROSY[15N] _Sample_label $sample_1 save_ save_1H-JR[15N]_6 _Saveframe_category NMR_applied_experiment _Experiment_name 1H-JR[15N] _Sample_label $sample_1 save_ save_NOESY[15N]-Imino_7 _Saveframe_category NMR_applied_experiment _Experiment_name NOESY[15N]-Imino _Sample_label $sample_1 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units 'ionic strength' 75 . mM pH 6.2 . pH pressure 1 . atm temperature 298 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_shift_reference_1 _Saveframe_category chemical_shift_reference _Details . loop_ _Mol_common_name _Atom_type _Atom_isotope_number _Atom_group _Chem_shift_units _Chem_shift_value _Reference_method _Reference_type _External_reference_sample_geometry _External_reference_location _External_reference_axis _Indirect_shift_ratio DSS C 13 'methyl protons' ppm 0.00 na indirect . . . 0.251449530 DSS H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000 DSS N 15 'methyl protons' ppm 0.00 na indirect . . . 0.101329118 stop_ save_ ################################### # Assigned chemical shift lists # ################################### ################################################################### # Chemical Shift Ambiguity Index Value Definitions # # # # The values other than 1 are used for those atoms with different # # chemical shifts that cannot be assigned to stereospecific atoms # # or to specific residues or chains. # # # # Index Value Definition # # # # 1 Unique (including isolated methyl protons, # # geminal atoms, and geminal methyl # # groups with identical chemical shifts) # # (e.g. ILE HD11, HD12, HD13 protons) # # 2 Ambiguity of geminal atoms or geminal methyl # # proton groups (e.g. ASP HB2 and HB3 # # protons, LEU CD1 and CD2 carbons, or # # LEU HD11, HD12, HD13 and HD21, HD22, # # HD23 methyl protons) # # 3 Aromatic atoms on opposite sides of # # symmetrical rings (e.g. TYR HE1 and HE2 # # protons) # # 4 Intraresidue ambiguities (e.g. LYS HG and # # HD protons or TRP HZ2 and HZ3 protons) # # 5 Interresidue ambiguities (LYS 12 vs. LYS 27) # # 6 Intermolecular ambiguities (e.g. ASP 31 CA # # in monomer 1 and ASP 31 CA in monomer 2 # # of an asymmetrical homodimer, duplex # # DNA assignments, or other assignments # # that may apply to atoms in one or more # # molecule in the molecular assembly) # # 9 Ambiguous, specific ambiguity not defined # # # ################################################################### save_assigned_chemical_shifts_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Software_label $software_2 stop_ loop_ _Experiment_label HNN-COSY[15N] NOESY[15N]CPMG HSQC[15N]-Amino HSQC[15N]-2J TROSY[15N] 1H-JR[15N] NOESY[15N]-Imino stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chem_shift_reference_1 _Mol_system_component_name 3_s2m _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 -1 1 G H1 H 13.3844 . 1 2 -1 1 G N1 N 148.356 . 1 3 -2 2 G H1 H 12.8168 . 1 4 -2 2 G N1 N 147.495 . 1 5 29728 3 U H3 H 14.3213 . 1 6 29728 3 U N3 N 162.547 . 1 7 29729 4 U H3 H 13.7411 . 1 8 29729 4 U N3 N 162.969 . 1 9 29730 5 C H6 H 7.853 . 1 10 29730 5 C H41 H 8.342 . 1 11 29730 5 C H42 H 6.9132 . 1 12 29730 5 C N3 N 196.658 . 1 13 29730 5 C N4 N 97.4564 . 1 14 29731 6 A H2 H 7.28383 . 1 15 29731 6 A N1 N 221.028 . 1 16 29731 6 A N3 N 212.332 . 1 17 29732 7 C H6 H 7.324 . 1 18 29732 7 C H41 H 8.0974 . 1 19 29732 7 C H42 H 6.95475 . 1 20 29732 7 C N3 N 196.03 . 1 21 29732 7 C N4 N 97.96 . 1 22 29739 14 C N3 N 193.726 . 1 23 29740 15 A H2 H 7.38517 . 1 24 29740 15 A N1 N 218.853 . 1 25 29740 15 A N3 N 211.22 . 1 26 29741 16 C N3 N 196.545 . 1 27 29743 18 C H6 H 7.742 . 1 28 29743 18 C H41 H 8.1214 . 1 29 29743 18 C H42 H 6.75175 . 1 30 29743 18 C N3 N 195.616 . 1 31 29743 18 C N4 N 97.5476 . 1 32 29744 19 G H1 H 12.1128 . 1 33 29744 19 G N1 N 147.128 . 1 34 29754 29 C N3 N 195.904 . 1 35 29755 30 G H1 H 11.8594 . 1 36 29755 30 G N1 N 145.959 . 1 37 29756 31 A H2 H 7.55478 . 1 38 29756 31 A N1 N 221.894 . 1 39 29756 31 A N3 N 215.536 . 1 40 29757 32 G H1 H 12.7032 . 1 41 29757 32 G N1 N 148.16 . 1 42 29758 33 U H3 H 13.941 . 1 43 29758 33 U N3 N 162.011 . 1 44 29759 34 G H1 H 13.0219 . 1 45 29759 34 G N1 N 148.323 . 1 46 29764 39 G H1 H 13.2635 . 1 47 29764 39 G N1 N 148.683 . 1 48 29765 40 U H3 H 13.5157 . 1 49 29765 40 U N3 N 161.977 . 1 50 29766 41 G H1 H 11.6245 . 1 51 29766 41 G N1 N 146.277 . 1 52 29767 42 A H2 H 7.04367 . 1 53 29767 42 A N1 N 220.367 . 1 54 29767 42 A N3 N 211.243 . 1 55 29768 43 A H2 H 7.7655 . 1 56 29768 43 A N1 N 221.673 . 1 57 29768 43 A N3 N 211.095 . 1 58 1 44 C H6 H 7.409 . 1 59 1 44 C H41 H 8.3452 . 1 60 1 44 C H42 H 6.9515 . 1 61 1 44 C N3 N 197.577 . 1 62 1 44 C N4 N 98.6692 . 1 63 2 45 C N3 N 196.443 . 1 stop_ save_